I have no idea what you had in mind... Placing the NTCONFIG.POL file in a subdir and setting the path as manual, is identical to placing it in NetLogon and leaving the clients on automatic. I presume you are wanting to implent the NT4-style policies because you are on an NT4 domain and possibly with Win9x and NT4 clients.
In AD, the GPOs are stored on SysVol and not in \NetLogon and they only work on W2K/XP/W2K3. THere is no support for Wintendo or NT4.
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